MrHedmad

MrHedmad, 1 month ago to random

I'm looking at the expression of genes across many different tumor types and studies and it looks to me like there is very little consensus overall. Should I be scared?

MrHedmad, 3 months ago to bluesky

So, what's everyone's opinion on #bluesky ?

Elendol, 3 months ago to random

Ffs, I thought Python virtual environments would be more stable. Poetry executables from my shell and another from a container are fighting over the lockfike and installed dependencies...

MrHedmad, 4 months ago to bioinformatics

My #PhD program allows me to spend up to 6 months abroad to work on anything I'd like (with my supervisors approval).

I'd like to spend them in the #openscience and #researchsoftwareengineering fields. If anyone has some ideas of whom I could contact I'd be grateful.

My about page: https://mrhedmad.github.io/blog/about/

#bioinformatics #research #DataStewardship

MrHedmad, 6 months ago to rust

I'm in the middle of my first, real, actual #rust project, a weird project management tool that follows how I structure and execute my own bioinformatics analyses.

I've started by writing a README as if the tool was already made, so I could get my head straight on what I wanted to make, and now I'm implementing it!

I know very little rust, so if any kind soul wants to to review my code and suggest better ways to do the stuff I'm doing, I'd be forever grateful!

https://github.com/MrHedmad/kerblam

MrHedmad, 7 months ago to bioinformatics

I need to create a very simple GUI application that boils down to basically an HTML form but local.

Any suggestions on what to use to make it? I'm familiar with Python but I want to make it as portable and as cross platform as possible. A Web application would be perfect but I have absolutely no knowledge about making websites, and I don't want a hosted solution.

Any tips?

#bioinformatics #programming #help

Elendol, 8 months ago to random

Blessed are the projects that don't rely on conda.

MrHedmad, 10 months ago to random

I'm trying #obsidian and it's blowing my mind! (so many mind blows this week)

It integrates bullet journaling, handfree writing on my ipad, has templates tags, powerful search, and makes knowledge graphs by default!

You can also link to pages that you haven't written yet so you can go back later and continue filling in the gaps.

Syncing notes is a problem though, and you're basically forced to use their sync function, which costs a bit. You get a 40% discount if you're an academic though.

MrHedmad, 11 months ago to Help

I've been thinking and reading a bit about data stewardship and the role of data stewards.

I like it. I really like it. I am pretty sure I would like to do it as a job.

But I have no idea how to "formally" prepare for it. Are there any data stewards in the academic setting that would like to chat?

Please.
Pretty please.

#openscience #data #datastewards #DataStewardship #help #plsboost

MrHedmad, 1 year ago to random

Do you use Continuous Integration in your #bioinformatics or #datascience projects or know of projects that do? If so, can you provide the link to the example? If not, why? Do you feel it would take too much time?

MrHedmad, 1 year ago to random

Nature: "As a journal, Nature Genetics is fully supportive of open science and we encourage our authors to bear this in mind when conducting their research, for the betterment of the field as a whole."

Also Nature: charges 11 grand to open access a paper in hybrid journals

(Probably) paywalled editorial: https://www.nature.com/articles/s41588-023-01411-0

#OpenScience

mmasnick, 1 year ago to random

Okay folks: this morning we're launching something we think is pretty useful. Lots of people have strong opinions on how content moderation should work, but they've never done it. So we built a content moderation mobile game (browser-based): https://moderatormayhem.engine.is/

Details about it are here: https://www.techdirt.com/2023/05/11/moderator-mayhem-a-mobile-game-to-see-how-well-you-can-handle-content-moderation/

janriemer, 1 year ago (edited 1 year ago) to random

Do NOT use #gmail!

Edit: The following is NOT true. See edit below.

Gmail has just declared a very lengthy e-mail of mine as "SPAM". My recipient uses gmail, so I can't send them my message.

Thank you #Google for #censoring me and wasting my time!

Edit: I've tried to sent the e-mail to a non-gmail address and I experience the same issue. So it's NOT a gmail problem.

Sorry, for the confusion and the false accusation.😳

MrHedmad, 1 year ago to random

I have a very large .csv file with a numerical matrix saved within. I need to calculate the mean of many selections of values in each row. (e.g. In each row, the mean of the values at index 1, 3, 52, 123; then, in the same line, values 2, 3, 12, 29, 67, etc...)

My file is HUGE, even in row length (a row has like, 8000+ items), so I need this to be fast. I know the indexes I need to average at the start of the computation, but don't have enough memory to load the whole file at once.

MrHedmad, 1 year ago to mastodon

I forgot to do this, so here it is:
Hello #mastodon! I'm Luca, a #PhD student in #complexsystems at the University of Turin (#unito).

I mainly work in #genomics and #transcriptomics. My project involves the study of the #cancer #transportome, and its role in the overall #cellbiology.
I code in #python and #R, but i'm trying to (slowly) learn about #rustlang. I use #archlinux, btw.

I also play a ton of #boardgames and #videogames. I love #mechanicalkeyboard (s) and own a #corne myself.